Download The Process Diagram

The Process Diagram: Rational and Definition
Dec. 2004
The Process Diagram: Rationale and Definition
Hiroaki Kitano, Yukiko Matsuoka, Kanane Oda, Akira Funahashi
The Systems Biology Institute
This document describes rational behind “the process diagram”, and a set of symbols and
conventions that are implemented in CellDesignerTM 2.0 and possible extensions for CellDesignerTM
2.5 to be released in 2005.
1. Rationale Behind the Notation
Most diagrams in published papers are drawn using informal notations with sets of arrows,
bar-headed lines, and circles roughly representing activation, inhibition, and the proteins involved,
respectively. Fig. 1 is a typical example of just such a diagram for a MAPK cascade in a mammalian
cell.
Fig. 1. An example of informal arrows-and-bars diagram
In this diagram, the arrows may implicate several different reactions. For example, the arrow
from Ras to Raf (marked as 1 in Fig. 1) appears to indicate that Ras activates Raf. However, in
reality, Ras enhances plasma membrane translocation of Raf. Thus, this arrow is more accurate to be
read as “recruitment” or “translocation”, instead of activation. Two arrows originating from ERK to
RSK and c-Myc (marked as 2 in Fig. 1) are interpreted as activation of RSK and c-Myc by ERK.
However, the same representation could also be interpreted as one complex (ERK) that splits into
two subcomponents (RSK and c-Myc). The reason that we exclude this interpretation is because we
already know some of the properties of the components involved, not because of anything within the
diagram itself. How should we interpret the arrow leading from RSK to RSK (marked as 3 in Fig.
1
The Process Diagram: Rational and Definition
Dec. 2004
1)? In this case, the arrow is meant to be read as the translocation of RSK from cytosol to nucleus,
instead of activation of RSK by RSK itself. Therefore, among these simple examples, there are three
possible interpretations of the same arrow symbol; activation, dissociation, and translocation.
Not only are notations used with multiple meanings, the notation is ambiguous and unable to
represent essential information (and therefore not machine readable). Correct interpretation depends
upon the reader’s foreknowledge. For example, two arrows leading to Raf from PKC and Src
indicate the activation of Raf by these two kinases. However, it is unclear what the mechanisms are,
which residues are phosphorylated, or which is the first modulator of Raf. Accompanying text can
supplement missing information to explain otherwise ambiguous points. However, in some cases the
text might be more ambiguous than diagrams.
Kurt Kohn may have been the first to propose well-defined canonical representations for
molecular interactions (Kohn 1999; Kohn 2001); and other researchers have been working on
alternative representations (Pirson, Fortemaison et al. 2000; Cook, Farley et al. 2001; Maimon and
Browning 2001). Unfortunately, none of the proposals has been widely used for a variety reasons.
For example, there is no software tool to create a Kohn Map efficiently, and this type of
representation does not allow for explicit display of temporal processes. Other notations have
different shortcomings.
Circuit schematics used in electronics are ideal examples of information display in a
graphical but unambiguous manner. Engineers can reproduce the circuits drawn in the schematics
simply from the information contained in the diagram. Although the interactions may be
substantially more complex, one of our first goals in systems biology is to create standard graphical
notations that unambiguously represent molecular interactions of biological systems.
2. A Process Diagram
A successful graphical notation must: (1) allow representation of diverse biological objects
and interactions, (2) be semantically and visually unambiguous, (3) be able to incorporate notations,
(4) allow tools to convert a graphically represented model into mathematical formulas for analysis
and simulation, and (5) have software support to draw the diagrams. Although several graphical
notation systems have been already proposed (Kohn 1999; Pirson, Fortemaison et al. 2000; Cook,
Farley et al. 2001; Kohn 2001; Maimon and Browning 2001), each has obstacles to becoming a
standard. Kitano proposed a graphical notation for biological networks (Kitano 2003) designed to
express sufficient information in clearly visible and unambiguous way. Using the process diagram
2
The Process Diagram: Rational and Definition
Dec. 2004
notation, the molecular interactions shown in Fig. 1 can be graphically represented as shown in Fig.
2.
Fig. 2. A process diagram with a consistently defined notation
c-Myc :
CREB :
ERK :
MKK :
PDK1 :
PKC :
Raf :
Ras :
RSK :
SOS :
Src :
Fig.1, Fig.2 - Abbreviations
v-myc myelocytomatosis viral oncogene homolog
cAMP responsive element binding protein
extracellular signal-regulated kinase
mitogen-activated protein kinase kinase
pyruvate dehydrogenase kinase, isoenzyme 1
protein kinase C
v-raf-1 murine leukemia viral oncogene
related RAS viral (r-ras) oncogene homolog
ribosomal protein S6 kinase, 90kDa
son of sevenless
v-src sarcoma viral oncogene homolog
The process diagram is a state transition diagram that represents transition of the state of each
molecule using arrows that indicate transition and circle-headed arrows and bar-headed arrows to
specify promotion and inhibition of such transitions. The filled arrow (blue) in Fig. 1 is replaced by
an open arrow and a circle-headed line in Fig. 2. This indicates translocation of Raf from the cytosol
to plasma membrane and the circle-headed line (blue) from Ras to the open arrow indicates that Ras
promotes translocation of Raf to plasma membrane, where Raf is full-activated via phosphorylation
on both Tyr341 and Ser338 residues by Src and PKC, respectively. Indeed, the interaction of Ras
with Raf is generally indicated by an arrow used for activation, but this process is actually the
translocation of Raf, which is stimulated by Ras. Each of the two arrows (light green) originating
from ERK to RSK and c-Myc in Fig. 1 is represented in a very different way. The arrow heading to
RSK is replaced by a circle-headed line which indicates that RSK is phosphorylated by ERK, and
3
The Process Diagram: Rational and Definition
Dec. 2004
subsequently stimulates its auto-phosphorylation. The three filled arrows (light green) between four
RSK nodes indicate the state transitions caused by phosphorylation. Each state of phosphorylation
can be described sequentially. On the other hand, the pathway from ERK to c-Myc is interpreted as
ERK homodimer formation and translocation to the nucleus, where homodimerized ERK activates
c-Myc. When the reaction is described in this manner, an interpretation such as “one complex (ERK)
split into two subcomponents (RSK and c-Myc)” is impossible. The translocation of RSK from
cytosol to nucleus is shown with the open arrow (orange) and can be easily distinguished from state
transition or catalysis.
Overall, all reactions are easy to understand at a glance compared with the conventional
informal notation. The notation also shows specific characteristics of a protein. For example, readers
can quickly recognize that SOS is a guanine nucleotide exchange factor for Ras just by looking at
this diagram because sufficient information is presented. We believe that our notation could be a
convenient tool to enable researchers to share information involved in molecular interactions with
each other.
It is important to remind that the process diagram is a state transition diagram. Each node
represents state of molecule and complex. Arrow represents state transition among states of molecule.
In the conventional diagrams, arrow generally means “activation” or “inhibition” of the molecule.
The readers wish to know why “arrows” should be state-transition, instead of activation or inhibition
as seen in most informal diagrams. We believe that use the arrows in conventional diagram confuse
semantic of the symbol as well as limiting possible molecular processes that can be represented. For
example, a process of M-phase promoting factor (MPF), Cdc2 and Cdc13 complex, activation in cell
cycle, kinase such as Wee1 phosphorylates Tyr15 and Thr14 residues of Cdc2 that is one of
components for MPF (Den Haese, Walworth et al. 1995) (Fig. 3). However, MPF is not yet activated
by this phosphorylation. CAK also phosphorylates the other residue, Thr167, but not activate MPF
complex. Only when Cdc25 dephosphorylates two Thr15 and Thr14 residues of Cdc2, MPF is
activated (Fleig and Gould 1991; Gould, Moreno et al. 1991; Sveiczer, Tyson et al. 2004). If we use
“arrow” for activation, only interaction between MPF and Cdc25 can be described. In the process
diagram, whether a molecule is “active” or not is represented as a state of the note, instead of
“arrow” symbol for activation. Promoting and inhibition of state transition are represented as
modifier of state transition using a circle-headed arrow and a bar-headed arrow, respectively.
Using the process diagram, large scale molecular interaction process map with the size of
approximately 600 components and interactions have been developed which demonstrates scalability
of the notation (Kitano, Oda et al. 2004; Oda, Kimura et al. 2004).
4
The Process Diagram: Rational and Definition
Dec. 2004
Fig. 3. A process diagram representation of MPF cycle
APC :
CAK :
Cdc (2/13/25) :
Plo1 :
PP2A :
Rum1 :
Slp1 :
Wee1 :
Fig.3 - Abbreviations
anaphase promoting complex
cyclin-dependent kinase-activating kinase
cell division cycle (2/13/25)
polo kinase 1
protein phosphatase 2A
an inhibitor of Cdc13/Cdc2
sloppy-paired 1
mitosis inhibitor protein kinase wee1
3. Diagram Legends
The symbols used to represent molecules and interactions are shown in Fig. 3. Each
round-cornered box represents a specific state of a molecular species. The closed arrows (arrow head
filled) represent changes in the state of modification (or allostericity), rather than indicating
activation (as in Fig. 1). The schema avoids using symbols that directly point to the molecule to
indicate activation and inhibition. Instead, the diagram directly indicates a transition from an inactive
5
The Process Diagram: Rational and Definition
Dec. 2004
to an active state for activation, and a transition from an active state to an inactive state for inhibition.
When these transitions are promoted or inhibited by other mediating molecules, such as active
kinases, these reactions are represented by circle-headed lines for activation and bar-headed lines for
inhibition, respectively. An open arrow (arrow head not filled) indicates the translocation of a
molecule.
Fig. 4, 5, 6 indicate symbols used in the process diagram that is now employed in
CellDesigner 2.0 (Funahashi and Kitano 2003).
Fig. 4. Main symbols adopted by the CellDesigner’s Process Diagram
Fig. 5. Expressions of the inner structures and the states
6
The Process Diagram: Rational and Definition
Dec. 2004
Fig. 6. Residue modification
4. Simple Examples
A couple of simple examples would help readers to understand how to create the process
diagram. First, interaction involved in guanine nucleotide binding protein (G protein) is shown in Fig
7. In this diagram dissociation and reassociation of G protein heterotrimers composed of α-, β-,
γ-subunits is represented. β2-agonist ligand binding to β2-adrenoreceptor (β2-AR) which is a kind of
G-protein coupled receptor (GPCR) triggers the exchange of GTP for GDP on the αs-subunit,
resulting in dissociation of αs-subunit from βγ complex. This process is described as active β2-AR
catalysis (using a circle headed arrow) dissociation of GDP from Gαs, association of GTP with Gαs,
and dissociation of αs-GTP and βγ complex. Dissociated αs-GTP and βγ complex exhibit the ability
to interact with distinct effectors, such as adenylate cyclase, (shown as dashed line around the
rounded-corner box for Gαs and Gβγ) leading a series of downstream signal transduction pathways.
Gαs, however, has intrinsic GTPase activity which hydrolyzes GTP to GDP on the Gαs, (shown as
circle headed arrow from Gαs) so that Gαs is deactivated and inactive Gαsβγ complex is reassembled
(Wess 1997) (Johnson 1998). Other proteins, such as regulator of G-protein signalling (RGS) and β
adrenergic receptor kinase (βARK), are also involved in this process, but they are not shown in the
Fig. 7 for the sake of simplicity. Details of such activation and dissociation cannot be described
properly in informal diagrams.
7
The Process Diagram: Rational and Definition
Dec. 2004
Fig. 7. An example of the process diagram for G protein interactions
Second example shown in Fig. 8 is NF-κB related interaction. NF-κB is a dimeric
transcription factor and this diagram shows NF-κB signaling by prototypical p65/p50 heterodimer.
NF-κB p65/p50 is retained inactive by its association with IκBα, an inhibitor of NF-κB, and PKAc, a
catalytic subunit of protein kinase A. Ser32 and Ser36 residues of IκBα are phosphorylated by
IKKαβγ complex activated by NIK, which causes nuclear translocation of the NF-κB complex.
Translocation is shown using an open arrow. Lys21 and Lys22 residues on IκBα are
polyubiquitinated by SCFβ-TrCP (a RING E3 protein composed of β-TrCP, Skp1, Cul1, and RING
protein Roc1) and E2 ubiquitin-conjugating enzyme UbcH5, which causes nuclear export of the
complex and dissociation of IκBα followed proteasomal degradation (Ben-Neriah 2002). This results
in restoration of PKAc kinase activity to phosphorylate NF-κB Ser276 residue and phosphorylation
of Ser529 residue by CKII, which dramatically increases the transcriptional activity of NF-κB and
causes homodimerization. Then activated homodimer NF-κB is translocated into nucleus and
initiates transcription of target genes, such as IκBα and p50 (McKay and Cidlowski 1999; Ghosh and
Karin 2002).
8
The Process Diagram: Rational and Definition
Dec. 2004
Fig 8. An example of NF-κB related interactions
β-TrCP :
CKII :
IκBα :
IKK (α/β/γ) :
NF-κB :
NIK :
PKAc :
SCF :
UbcH5 :
Fig.8 - Abbreviations
β-transducin repeat containing protein
casein kinase II
nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor α
IκB kinase (α/β/γ)
nuclear factor-κB
NF-κB-inducing kinase
cAMP-dependent protein kinase catalytic subunit
SKP1-cullin-F-box
ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)
5. Future Extensions: Redefinition of Transcription, Translation Processes, and
Hierarchical Complex Representation
The problem of current process diagram is that transcription and translation processes are not
well defined. While the diagram is defined as state transition diagram, transcription and translation
9
The Process Diagram: Rational and Definition
Dec. 2004
processes use arrows as transcriptional activation and translational activation that is not consistent
with other part of the diagram. In the future release of CellDesigner (expected in Version 2.5), the
process diagram notation is extended and redefined to enhance representation capability for
transcription and translation processes.
5.1 Transcription and Translation Processes
For a simple description of transcription, genes are represented as simple rectangular boxes
and transcription factors and other regulatory factors bind to the box. A dashed arrow that represents
transcription process is used to indicate RNA is transcribed from the sequence and RNA translated
into protein (Fig. 9). Transcription and translation processes are represented with special arrows that
should represents complex processes behind it.
Fig. 9. A simple example of a CREB driven transcription process
Fig.10 represents more detail of this process. As a state transition diagram transcription
shall be described as transition of nucleotides into RNA, and translation shall be transition of amino
acid into protein. Fig.10 explicitly represent these processes. However, in many cases, such
processes do not need to be explicitly represented, so that we will define dedicated symbols for
simplify the user’s work, as seen in Fig. 9. Specific symbols for transcription and translation will be
defined by the time of CellDesigner 2.5 release.
Fig. 10. CREB driven transcription process with transcription machinery represented
Fig.9, 10
CBP/p300 :
TBP :
TFII (A/B/F/H) :
TIF2 :
PolII :
CREB binding protein
TATA box binding protein
general transcription factor II (A/B/F/H)
nuclear receptor coactivator 2
RNA polymerase II
10
The Process Diagram: Rational and Definition
Dec. 2004
5. 2 Promoter Structure Representations
A new extension allows user to define structure of promoter region, exon, and histons.
Specific promoter regions, exon, and histon are represented on upper part of the box (Fig. 11). When
such structure information is defined, lines for both sides and lower part of the box are either not
shown or dimmed to highlight structures represented on the upper line.
Fig. 11. New notation for transcription and translation
Fig. 12(a) indicates a set of new symbols for transcription, and Fig. 12(b) shows how it may
be used.
Fig. 12(a). Symbols related to transcription and translation
Fig. 12(b). A usage example transcription related symbols
With using detailed notation for promoter region, detailed state transition for transcription
11
The Process Diagram: Rational and Definition
Dec. 2004
can be described. Fig. 13 shows example of state transition of transcription factor bindings and a
transcription process.
Fig. 13. A process of transcription in the process diagram
12
The Process Diagram: Rational and Definition
Dec. 2004
5.3 RNA
RNA is represented in a slanted box. When exon structure is represented, exons are
represented on the upper line (Fig. 14).
Fig. 14. Representation of exon structure of RNA
Alternative splicing can be represented as transition of RNA from original state to multiple
RNA with different splicing patterns (Fig. 15).
Fig. 15. Alternative splicing example
5.4 Hierarchical Complex Representation
Current notation describe complex as simple association of multiple protein symbols. However, this
is not convenient when complex itself has distinct name. For example, NF-κB is a heterodimer of
p65 and p50. Current notation can only represent NF-κB as one elementary protein or as a complex
of p65 and p50 without naming then as NF-κB. Practical compromise is to name each subunit as
NF-κB (p65) and NF-κB (p50), but far from satisfactory. Many receptors are complex of subunits
each has its own name, so that this complex naming is a major problem is proper and convenient
description. In order to solve this problem, hierarchical complex representation will be introduced
that enables users to name both subunits and complex. Fig. 16 shows examples of such complex
description.
13
The Process Diagram: Rational and Definition
Dec. 2004
Fig. 16. Examples of Hierarchical complex description
Kir6.2 :
SUR1 :
Fig.16 - Abbreviations
potassium inwardly-rectifying channel , subfamily J, member 11
sulfonylurea receptor 1
6. Final Remarks
Graphical notations described in this document have been implemented in CellDesigner 2.0,
and extensions specified will be implemented in CellDesigner 2.5 that will be released in 2005. We
recognize that there are numbers of improvements needed to fully describe biological processes.
Thus, we would like to welcome comments and suggestions for improving graphical notations and
CellDesigner software. Our hope is to contribute to the community by offering possible standard set
of graphical notations that are powerful, software supported, and mathematically transportable.
REFERENCES
Ben-Neriah, Y. (2002). "Regulatory functions of ubiquitination in the immune system." Nat
Immunol 3(1): 20-6.
Cook, D. L., J. F. Farley, et al. (2001). "A basis for a visual language for describing, archiving
and analyzing functional models of complex biological systems." Genome Biol 2(4):
RESEARCH0012.
Den Haese, G. J., N. Walworth, et al. (1995). "The Wee1 protein kinase regulates T14
phosphorylation of fission yeast Cdc2." Mol Biol Cell 6(4): 371-85.
Fleig, U. N. and K. L. Gould (1991). "Regulation of cdc2 activity in Schizosaccharomyces
pombe: the role of phosphorylation." Semin Cell Biol 2(4): 195-204.
Funahashi, A. and H. Kitano (2003). "CellDesigner: a process diagram editor for
gene-regulatory and biochemical networks." Biosilico 1(5): 159-162.
Ghosh, S. and M. Karin (2002). "Missing pieces in the NF-kappaB puzzle." Cell 109 Suppl:
S81-96.
Gould, K. L., S. Moreno, et al. (1991). "Phosphorylation at Thr167 is required for
14
The Process Diagram: Rational and Definition
Dec. 2004
Schizosaccharomyces pombe p34cdc2 function." Embo J 10(11): 3297-309.
Johnson, M. (1998). "The beta-adrenoceptor." Am J Respir Crit Care Med 158(5 Pt 3):
S146-53.
Kitano, H. (2003). "A graphical notation for biochemical networks." BioSilico 1(5): 169-76.
Kitano, H., K. Oda, et al. (2004). "Metabolic syndrome and robustness tradeoffs." Diabetes
53 Suppl 3: S6-S15.
Kohn, K. W. (1999). "Molecular interaction map of the mammalian cell cycle control and
DNA repair systems." Mol Biol Cell 10(8): 2703-34.
Kohn, K. W. (2001). "Molecular interaction maps as information organizers and simulation
guides." Chaos 11(1): 84-97.
Maimon, R. and S. Browning (2001). Diagramatic Notation and Computational Structure of
Gene Networks. Proceedings of the Second International Conference on Systems
Biology. H. Kitano. Madison, WI, Omnipress: 311-7.
McKay, L. I. and J. A. Cidlowski (1999). "Molecular control of immune/inflammatory
responses: interactions between nuclear factor-kappa B and steroid
receptor-signaling pathways." Endocr Rev 20(4): 435-59.
Oda, K., T. Kimura, et al. (2004). "Molecular Interaction Map of a Macrophage." AfCS
Research Reports 2(14 DA): 1-12.
Pirson, I., N. Fortemaison, et al. (2000). "The visual display of regulatory information and
networks." Trends Cell Biol 10(10): 404-8.
Sveiczer, A., J. J. Tyson, et al. (2004). "Modelling the fission yeast cell cycle." Brief Funct
Genomic Proteomic 2(4): 298-307.
Wess, J. (1997). "G-protein-coupled receptors: molecular mechanisms involved in receptor
activation and selectivity of G-protein recognition." Faseb J 11(5): 346-54.
15
The Process Diagram: Rational and Definition
Dec. 2004
[Abbreviation List]
Abbreviation
APC
CAK
CBP/p300
Cdc (2/13/25)
CKII
c-Myc
CREB
ERK
IKK (α/β/γ)
IκBα
Kir6.2
MKK
NF-κB
NIK
PDK1
PKAc
PKC
Plo1
PolII
PP2A
Raf
Ras
RSK
Rum1
SCF
Slp1
SOS
Src
SUR1
TBP
TFII (A/B/F/H)
TIF2
UbcH5
Wee1
β2-AR
β-TrCP
Name
anaphase promoting complex
cyclin-dependent kinase-activating kinase
CREB binding protein
cell division cycle (2/13/25)
casein kinase II
v-myc myelocytomatosis viral oncogene homolog
cAMP responsive element binding protein
extracellular signal-regulated kinase
IκB kinase (α/β/γ)
nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor α
potassium inwardly-rectifying channel , subfamily J, member 11
mitogen-activated protein kinase kinase
nuclear factor-κB
NF-κB-inducing kinase
pyruvate dehydrogenase kinase, isoenzyme 1
cAMP-dependent protein kinase catalytic subunit
protein kinase C
polo kinase 1
RNA polymerase II
protein phosphatase 2A
v-raf-1 murine leukemia viral oncogene
related RAS viral (r-ras) oncogene homolog
ribosomal protein S6 kinase, 90kDa
an inhibitor of Cdc13/Cdc2
SKP1-cullin-F-box
sloppy-paired 1
son of sevenless
v-src sarcoma viral oncogene homolog
sulfonylurea receptor 1
TATA box binding protein
general transcription factor II (A/B/F/H)
nuclear receptor coactivator 2
ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)
mitosis inhibitor protein kinase wee1
β2-adrenoceptor
β-transducin repeat containing protein
16
Figure#
Fig.3
Fig.3
Fig.9
Fig.3
Fig.8
Fig.1 , Fig.2
Fig.1 , Fig.2
Fig.1 , Fig.2
Fig.8
Fig.8
Fig.16
Fig.1 , Fig.2
Fig.8
Fig.8
Fig.1 , Fig.2
Fig.8
Fig.1 , Fig.2
Fig.3
Fig.9
Fig.3
Fig.1 , Fig.2
Fig.1 , Fig.2
Fig.1 , Fig.2
Fig.3
Fig.8
Fig.3
Fig.1, Fig.2
Fig.1, Fig.2
Fig.16
Fig.9
Fig.9
Fig.9
Fig.8
Fig.3
Fig.7
Fig.8